PyDAIR 0.1.2

INSTALLTION

PyDAIR requires Python 2.7 together with NumPy, Pandas, matplotlib, and BioPython packages. Further, PyDAIR requires NCBI BLAST+ for aligning IGH sequence to germline databases. PyDAIR is avaliable on the PyPI repository, as well as can be installed like any other Python package using pip command.

pip install numpy --user
pip install pandas --user
pip install matplotlib --user
pip install biopython --user
pip install pydair --user

Installtion instructions for NCBI BLAST+ are available on NCBI website. User should follow the instruction to install NCBI BLAST+.

Usage

PyDAIR has two main commands that are pydair-parseseq and pydair-analysis.

pydair-parseseq identifies V, D, and J genes from IGH each sequence by aligning IGH sequence to germline (V, D, and J) database using NCBI BLAST+. It requires IGH sequences, germline sequences, BLAST databases of germiline sequences, and BLAST parameters. The sequences should be given by FASTA format.

pydair-parseseq -q input_igh_sequences.fa \
                -v v.fa                   \
                -d d.fa                   \
                -j j.fa                   \
                --v-blastdb blastdb_v     \
                --d-blastdb blastdb_d     \
                --j-blastdb blastdb_j     \
                -o output1

PyDAIR generates several files to save the intermediate results, such as BLAST results, region that cannot be aligned to V and J genes. The final result is saved into output1.pydair file. If there several samples, pydair-parseseq should be run several times for each sample.

The statistical summaries are calculated by pydair-analysis command.

pydair-analysis -i output1.pydair output2.pydair output3.pydair  \
                -n Fugu1 Fugu2 Fugu3                             \
                -o stats_result                                  \
                --contain_ambiguous_D