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simplify README
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dvklopfenstein committed Feb 5, 2024
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Expand Up @@ -77,24 +77,13 @@ or
```$ icite -H; icite 26032263 -r | sort -k6 -r```

## 4) Summarize a group of citations
* 4a) Examine a paper with PMID `30022098`. Print the column headers(`-H`):
`icite -H 30022098`
* 4b) Download the details about each paper(`-c`) that cites `30022098` into a file(`-o goatools_cites.txt`):
* 4a) Create a file containing numerous PMIDs annotated with icite info.
`icite 30022098 -c -o goatools_cites.txt`
* 4c) Summarize the overall performace of the 300+ citing papers contained in `goatools_cites.txt`
* 4b) Summarize the overall performace of the 300+ citing papers contained in `goatools_cites.txt`
`summarize_papers goatools_cites.txt -p TOP CIT CLI`

### 4a) Examine a paper with PMID `30022098`. Print the column headers(`-H`):
```
$ icite -H 30022098
COL 2 3 4 5 6 7 8 9 10 au[11](authors)
TYP PMID RP HAMCc % G YEAR cit cli ref au[00](authors) title
TOP 30022098 R. .A..c 100 4 2018 318 1 23 au[14](D V Klopfenstein) GOATOOLS: A Python library for Gene Ontology analyses.
```

Paper with PMID `30022098` is cited by `318`(`cit`) other research papers and `1`(`cli`) clinical study. It has `23` references(`ref`).

### 4b) Download the details about each paper(`-c`) that cites `30022098` into a file(`-o goatools_cites.txt`):
### 4a) Create a file containing numerous PMIDs annotated with icite info.
```
$ icite 30022098 -c -o goatools_cites.txt
```
Expand All @@ -114,7 +103,7 @@ $ grep CLI goatools_cites.txt | wc -l
1
```

### 4c) Summarize all the papers in `goatools_cites.txt`
### 4b) Summarize all the papers in `goatools_cites.txt`
**NEW FUNCTIONALITY; INPUT REQUESTED: What would you like to see?** [Open an issue](https://github.com/dvklopfenstein/pmidcite/issues) to comment.
```
$ summarize_papers goatools_cites.txt -p TOP CIT CLI
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