design/content-writing/pdf/SKILL.md
Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.
npx skillsauth add harsh040506/claude-code-unified-skill-plugin-library pdfInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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This guide covers essential PDF processing operations using Python libraries and command-line tools. For advanced features, JavaScript libraries, and detailed examples, see REFERENCE.md. If you need to fill out a PDF form, read FORMS.md and follow its instructions.
from pypdf import PdfReader, PdfWriter
# Read a PDF
reader = PdfReader("document.pdf")
print(f"Pages: {len(reader.pages)}")
# Extract text
text = ""
for page in reader.pages:
text += page.extract_text()
from pypdf import PdfWriter, PdfReader
writer = PdfWriter()
for pdf_file in ["doc1.pdf", "doc2.pdf", "doc3.pdf"]:
reader = PdfReader(pdf_file)
for page in reader.pages:
writer.add_page(page)
with open("merged.pdf", "wb") as output:
writer.write(output)
reader = PdfReader("input.pdf")
for i, page in enumerate(reader.pages):
writer = PdfWriter()
writer.add_page(page)
with open(f"page_{i+1}.pdf", "wb") as output:
writer.write(output)
reader = PdfReader("document.pdf")
meta = reader.metadata
print(f"Title: {meta.title}")
print(f"Author: {meta.author}")
print(f"Subject: {meta.subject}")
print(f"Creator: {meta.creator}")
reader = PdfReader("input.pdf")
writer = PdfWriter()
page = reader.pages[0]
page.rotate(90) # Rotate 90 degrees clockwise
writer.add_page(page)
with open("rotated.pdf", "wb") as output:
writer.write(output)
import pdfplumber
with pdfplumber.open("document.pdf") as pdf:
for page in pdf.pages:
text = page.extract_text()
print(text)
with pdfplumber.open("document.pdf") as pdf:
for i, page in enumerate(pdf.pages):
tables = page.extract_tables()
for j, table in enumerate(tables):
print(f"Table {j+1} on page {i+1}:")
for row in table:
print(row)
import pandas as pd
with pdfplumber.open("document.pdf") as pdf:
all_tables = []
for page in pdf.pages:
tables = page.extract_tables()
for table in tables:
if table: # Check if table is not empty
df = pd.DataFrame(table[1:], columns=table[0])
all_tables.append(df)
# Combine all tables
if all_tables:
combined_df = pd.concat(all_tables, ignore_index=True)
combined_df.to_excel("extracted_tables.xlsx", index=False)
from reportlab.lib.pagesizes import letter
from reportlab.pdfgen import canvas
c = canvas.Canvas("hello.pdf", pagesize=letter)
width, height = letter
# Add text
c.drawString(100, height - 100, "Hello World!")
c.drawString(100, height - 120, "This is a PDF created with reportlab")
# Add a line
c.line(100, height - 140, 400, height - 140)
# Save
c.save()
from reportlab.lib.pagesizes import letter
from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, PageBreak
from reportlab.lib.styles import getSampleStyleSheet
doc = SimpleDocTemplate("report.pdf", pagesize=letter)
styles = getSampleStyleSheet()
story = []
# Add content
title = Paragraph("Report Title", styles['Title'])
story.append(title)
story.append(Spacer(1, 12))
body = Paragraph("This is the body of the report. " * 20, styles['Normal'])
story.append(body)
story.append(PageBreak())
# Page 2
story.append(Paragraph("Page 2", styles['Heading1']))
story.append(Paragraph("Content for page 2", styles['Normal']))
# Build PDF
doc.build(story)
IMPORTANT: Never use Unicode subscript/superscript characters (₀₁₂₃₄₅₆₇₈₉, ⁰¹²³⁴⁵⁶⁷⁸⁹) in ReportLab PDFs. The built-in fonts do not include these glyphs, causing them to render as solid black boxes.
Instead, use ReportLab's XML markup tags in Paragraph objects:
from reportlab.platypus import Paragraph
from reportlab.lib.styles import getSampleStyleSheet
styles = getSampleStyleSheet()
# Subscripts: use <sub> tag
chemical = Paragraph("H<sub>2</sub>O", styles['Normal'])
# Superscripts: use <super> tag
squared = Paragraph("x<super>2</super> + y<super>2</super>", styles['Normal'])
For canvas-drawn text (not Paragraph objects), manually adjust font the size and position rather than using Unicode subscripts/superscripts.
# Extract text
pdftotext input.pdf output.txt
# Extract text preserving layout
pdftotext -layout input.pdf output.txt
# Extract specific pages
pdftotext -f 1 -l 5 input.pdf output.txt # Pages 1-5
# Merge PDFs
qpdf --empty --pages file1.pdf file2.pdf -- merged.pdf
# Split pages
qpdf input.pdf --pages . 1-5 -- pages1-5.pdf
qpdf input.pdf --pages . 6-10 -- pages6-10.pdf
# Rotate pages
qpdf input.pdf output.pdf --rotate=+90:1 # Rotate page 1 by 90 degrees
# Remove password
qpdf --password=mypassword --decrypt encrypted.pdf decrypted.pdf
# Merge
pdftk file1.pdf file2.pdf cat output merged.pdf
# Split
pdftk input.pdf burst
# Rotate
pdftk input.pdf rotate 1east output rotated.pdf
# Requires: pip install pytesseract pdf2image
import pytesseract
from pdf2image import convert_from_path
# Convert PDF to images
images = convert_from_path('scanned.pdf')
# OCR each page
text = ""
for i, image in enumerate(images):
text += f"Page {i+1}:\n"
text += pytesseract.image_to_string(image)
text += "\n\n"
print(text)
from pypdf import PdfReader, PdfWriter
# Create watermark (or load existing)
watermark = PdfReader("watermark.pdf").pages[0]
# Apply to all pages
reader = PdfReader("document.pdf")
writer = PdfWriter()
for page in reader.pages:
page.merge_page(watermark)
writer.add_page(page)
with open("watermarked.pdf", "wb") as output:
writer.write(output)
# Using pdfimages (poppler-utils)
pdfimages -j input.pdf output_prefix
# This extracts all images as output_prefix-000.jpg, output_prefix-001.jpg, etc.
from pypdf import PdfReader, PdfWriter
reader = PdfReader("input.pdf")
writer = PdfWriter()
for page in reader.pages:
writer.add_page(page)
# Add password
writer.encrypt("userpassword", "ownerpassword")
with open("encrypted.pdf", "wb") as output:
writer.write(output)
| Task | Best Tool | Command/Code |
|------|-----------|--------------|
| Merge PDFs | pypdf | writer.add_page(page) |
| Split PDFs | pypdf | One page per file |
| Extract text | pdfplumber | page.extract_text() |
| Extract tables | pdfplumber | page.extract_tables() |
| Create PDFs | reportlab | Canvas or Platypus |
| Command line merge | qpdf | qpdf --empty --pages ... |
| OCR scanned PDFs | pytesseract | Convert to image first |
| Fill PDF forms | pdf-lib or pypdf (see FORMS.md) | See FORMS.md |
testing
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
tools
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
testing
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.