transcriptome_microsats's Introduction

transcriptome_microsats

Scripts used in evaluating microsatellite loci developed from transcriptomes.

##Overview

These scripts were used to process the output of the microsatellite finding program MISA (Dieringer and Schlötterer, 2003). MISA was run on the transcriptome datasets from the 1,000 Plant Transcriptome Project and the results summarized with these and previously released scripts.

Please see the Tutorial for a walk through of developing microsatellite loci from a sample dataset and more complete usage and output information.

What follows is a brief description of the scripts available here.

Scripts and their functions:

LocateSSRsandORFs.py

A script to compare the location of an SSR and the longest ORF in a given scaffold. Note that for the project, ORFs were identified using get_orfs_or_cdss.py.

getScaffolds.py

A script to pull sequences from a fasta file based on a list and write to a new file.

SSR_RepeatFilter.py

Filters out microsatellite loci likely derived from inferred isoforms of the same locus.

compare_pcrs.py

Script to compare the ePCR results of amplifying one sample with the primers developed from another sample.

add_distances.py

Add genetic distance to table of microsats.

DiffMicrosatsBatch.R

This scrpt is summarizes the ePCR results. It generates a summary containing SSR and flanking region differences.

Graphs10GeneticID.R

Generates figure ## of Hodel et al 2015.

PAL_to_BLAST.R

This script takes a set of PALs (potentially amplifiable loci) from PAL_FINDER and removes duplicates. It then outputs a fasta file of the loci that can be used in a BLAST search.

BLAST_to_Coding_SSR.R

This script takes in a .gff annotated genome file from NCBI and BLAST results and creates the two input files for the script Coding_SSR.py

Coding_SSR.py

This script compares two input files--one ("query") containing the genomic locations of SSR loci identified, and one ("subject") containing the locations of translated regions of the genome (CDS).

Repeat_Numb_Search.R

This script uses the output from the script Coding_SSR.py and the program PAL_FINDER to identify the distribution of repeat motifs among the PALs.

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transcriptome_microsats's Issues

python get_orfs_or_cdss.py update broke tutorial

The tutorial was written with a version of the python get_orfs_or_cdss.py script from https://github.com/peterjc/pico_galaxy which was reconfigured in commit 732cf22 to use optparse.

Need to either update tutorial or point to older version of the script that was used.

The output file '*.Locations' for the script 'LocateSSRsandORFs.py' is very confusing

There seems to be an issue with the output '*.Locations' of the script 'LocateSSRsandORFs.py'. This output is supposed to summarize the locations of SSRs relative to the longest ORF on EACH scaffold. Instead, for EVERY SSR identified, the output shows the name of the LAST scaffold|ORF number in the first column; and in the sixth and seventh columns, respectively, the start and the end of the longest ORF on the last scaffold.

getting Error while running LocateSSRsandORFs.py

CAMMAND:
python ./LocateSSRsandORFs.py -i Pterocarpus_rohrii.ORFS.faa -r Pterocarpus_rohrii.fna.misa_SSR.results -o Pterocarpus_rohrii.Locations -s SSR_ORF_summary.txt

OUTPUT:
File "LocateSSRsandORFs.py", line 40
print "Can't open file", resultfile
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Can't open file", resultfile)?

I am getting this error, can anyone help with this?

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